Evidence map›Paper›PMID 24790824›Full record

ArticleSpringerPlus2014

Genetic diversity of rotavirus genome segment 6 (encoding VP6) in Pretoria, South Africa.

Martin M Nyaga, Mathew D Esona, Khuzwayo C Jere, Ina Peenze, Mapaseka L Seheri, M Jeffrey Mphahlele

Open access · diamondAbstract readCase Reports
PubMed Full text at PMC Publisher
In one paragraph

Article in SpringerPlus, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.4field-weighted citation impact, top 38% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed, 6 citations in OpenAlex.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors at 1 institution in 1 country.

Martin M NyagaMedical Research Council/Diarrhoeal Pathogens Research Unit, Department of Virology, Medunsa Campus, University of Limpopo/NHLS Dr George Mukhari Tertiary Laboratory, Pretoria, South Africa.
Mathew D EsonaMedical Research Council/Diarrhoeal Pathogens Research Unit, Department of Virology, Medunsa Campus, University of Limpopo/NHLS Dr George Mukhari Tertiary Laboratory, Pretoria, South Africa ; Gastroenteritis and Respiratory Viruses Laboratory Branch, Division of Viral Diseases, NCIRD, CDC, Atlanta, Georgia USA.
Khuzwayo C JereMedical Research Council/Diarrhoeal Pathogens Research Unit, Department of Virology, Medunsa Campus, University of Limpopo/NHLS Dr George Mukhari Tertiary Laboratory, Pretoria, South Africa ; Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
Ina PeenzeMedical Research Council/Diarrhoeal Pathogens Research Unit, Department of Virology, Medunsa Campus, University of Limpopo/NHLS Dr George Mukhari Tertiary Laboratory, Pretoria, South Africa.
Mapaseka L SeheriMedical Research Council/Diarrhoeal Pathogens Research Unit, Department of Virology, Medunsa Campus, University of Limpopo/NHLS Dr George Mukhari Tertiary Laboratory, Pretoria, South Africa.
M Jeffrey MphahleleMedical Research Council/Diarrhoeal Pathogens Research Unit, Department of Virology, Medunsa Campus, University of Limpopo/NHLS Dr George Mukhari Tertiary Laboratory, Pretoria, South Africa.
University of Limpopo · ZA

Funding

Wellcome Trust 101113
6 · The paper itself

Abstract

backgroundRotavirus viral protein 6 (VP6), encoded by genome segment (GS) 6, is the primary target for rotavirus diagnosis by serological and some molecular techniques. Selected full length nucleotide sequences of GS 6 of rotavirus strains from South Africa were sequenced and analysed to determine genetic diversity and variations within the circulating rotaviruses.

findingsThe VP6 amplicons were sequenced using the Sanger ABI 3130xl. Phylogenetic and pairwise analysis revealed that the VP6 genes of the study strains belonged to two different VP6 [I] genotypes. Five sequences were assigned genotype I1 and seven as genotype I2. Comparison of the group specific antigenic regions of the South African strains to the reference strains, shows that the South African VP6 sequences belonging to the VP6 genotype I2 were highly conserved, with only two amino acids changes at positions 239 (T›N) and 261(I›V). On the other hand, South African VP6 sequences belonging to I1 genotypes revealed several amino acid variations mostly within the antigenic region III.

conclusionsRotavirus strains with I1 and I2 genotype are predominantly circulating within the South African communities of which the later seems to be more conserved within the antigenic regions. The observed genetic variations observed within GS 6 of rotaviruses analysed in the current study are unlikely to impact negatively on the performance of the current VP6-based detection methods. Nevertheless, investigators should continually consider this diversity and adapt the primer design for the detection and characterization of the VP6 gene accordingly.

Indexed as

Genetic diversityPretoriaRotavirusesSouth AfricaViral protein 6

Identifiers

PMID24790824
PMCPMC4000354
OpenAlexW2098536545

What OpenQuestion holds

Textmetadata
LicenceCC BY
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.